11-119919359-A-G

Variant names:

• chr11-119919359-A-G
• rs10502232
• ENST00000662653.2:n.600-101A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000662653.2(ENSG00000288047):​n.600-101A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0263 in 152,308 control chromosomes in the GnomAD database, including 86 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.026 (86 hom., cov: 33)
• Consequence: ENSG00000288047 ENST00000662653.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 3 publications found

Genes affected

ENSG00000288047 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0263 (4002/152308) while in subpopulation NFE AF = 0.0387 (2630/68022). AF 95% confidence interval is 0.0374. There are 86 homozygotes in GnomAd4. There are 2007 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 86 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662653.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288047	ENST00000662653.2		n.600-101A>G		intron	N/A
	ENSG00000288047	ENST00000688572.2		n.780-101A>G		intron	N/A
	ENSG00000288047	ENST00000701780.1		n.779+5663A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0263 AC: 4004 AN: 152190 Hom.: 86 Cov.: 33

Gnomad AFR AF: 0.00610

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.0106

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.0187

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0263 AC: 4002 AN: 152308 Hom.: 86 Cov.: 33 AF XY: 0.0269 AC XY: 2007 AN XY: 74472

African (AFR) AF: 0.00609 AC: 253 AN: 41576

American (AMR) AF: 0.0106 AC: 162 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00186 AC: 9 AN: 4832

European-Finnish (FIN) AF: 0.0787 AC: 834 AN: 10602

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0387 AC: 2630 AN: 68022

Other (OTH) AF: 0.0185 AC: 39 AN: 2112

Alfa AF: 0.0341 Hom.: 191

Bravo AF: 0.0206

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.6
DANN	Benign	0.85
PhyloP100		0.082

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10502232; hg19: chr11-119790068;